Included libraries | Package variables | General documentation | Methods |
PFM | No description | Code |
_calculate_PFM | No description | Code |
get_sites | No description | Code |
new | No description | Code |
pattern | No description | Code |
PFM | description | prev | next | Top |
my ($self, %args) = @_; return TFBS::Matrix::PFM->new (-name => "unknown", -ID => "unknown", -class=> "unknown", -tags => { %{$self->{'tags'} } }, %args, -matrix => $self->_calculate_PFM() );}
_calculate_PFM | description | prev | next | Top |
# simplest case: matrix already IS PFM my $self = shift;}
return [@{$self->{'matrix'}}];
get_sites | description | prev | next | Top |
return @{$_[0]->{'sites'}}; } 1;}
new | description | prev | next | Top |
my ($caller, %args) = @_; #my $matrix = TFBS::Matrix->new(%args, -matrixtype=>"PFM");}
#my $self = bless $matrix, ref($caller) || $caller;
my $self = $caller->SUPER::new(%args, -matrixtype=>"PFM"); $self->{'length'} = $args{'-length'} || scalar @{$self->{'matrix'}->[0]}; $self->{'nr_hits'} = ($args{'-nr_hits'} || undef); # || $self->throw("No -nr_hits provided.");
# Why was nr_hits required ?? (Boris)
$self->{'sites'}=$args{'-sites'}; # $self->{'tags'} = ($args{'-tags'} || {});
return $self;
pattern | description | prev | next | Top |
my ($self, %args ) = @_; $self->PFM(%args);}